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The preparation of materials with a well-defined mesoporous structure and hydrophobicity is of great significance for heterogeneous catalyst development, yet there still remains a challenge for fabricating the above materials without using templates. Herein, the polymerization of L-proline-functionalized monomer with crosslinkers containing variable alkyl-bridged length (n = 2,4,6,8) and vinyl-modified Fe3O4 nanoparticles to construct mesoporous poly(L-proline)s (MPLPs) has been reported for the first time. The resultant MPLPs were analyzed by characterization methods, suggesting that MPLPs with a well-defined mesoporous structure and unique hydrophobicity were successfully constructed by synergistic regulation of vinyl-modified Fe3O4 nanoparticles and crosslinkers with alkyl-bridged length of 6 carbon atoms, in which vinyl-modified Fe3O4 nanoparticles as structural reinforcer plays a vital role for the mesoporous formation. Moreover, the resultant MPLPs were found to be efficient catalysts for one-pot synthesis of functionalized spiroindolones and olefins. The kinetic study and the water contact angle indicate the mesoporous confinement and hydrophobic micro-environment in organic transformations. Hence, the high activity of MPLPs is ascribed to synergistic effect of mesoporous confinement and hydrophobic micro-environment, and the adsorption experiment results further confirm this synergistic catalysis. This work promotes a textural engineering approach to the development of multifunctional materials with well-defined mesopores and hydrophobicity.

The liver is an important organ for drugs disposition, and thus how to accurately evaluate hepatic clearance is essential for proper drug dosing. However, there are many limitations in drug dosage adjustment based on liver function and pharmacogenomic testing. In this study, we evaluated the ability of endogenous glycochenodeoxycholate-3-sulfate (GCDCA-S) and 4β-hydroxycholesterol (4β-HC) plasma levels to evaluate organic anion-transporting polypeptide (Oatps)-mediated hepatic uptake and Cyp3a-meidated metabolism of atorvastatin (ATV) in rats. The concentration of ATV and its metabolites, 2-OH ATV and 4-OH ATV, was markedly increased after a single injection of rifampicin (RIF), an inhibitor of Oatps. Concurrently, plasma GCDCA-S levels were also elevated. After a single injection of the Cyp3a inhibitor ketoconazole (KTZ), plasma ATV concentrations were significantly increased and 2-OH ATV concentrations were decreased, consistent with the metabolism of ATV by Cyp3a. However, plasma 4β-HC was not affected by KTZ treatment despite it being a Cyp3a metabolite of cholesterol. After repeated oral administration of RIF, plasma concentrations of ATV, 2-OH ATV and 4-OH ATV were markedly increased and the hepatic uptake ratio of ATV and GCDCA-S was decreased. KTZ did not affect plasma concentrations of ATV, 2-OH ATV and 4-OH ATV, but significantly decreased the metabolic ratio of total and 4-OH ATV. However, the plasma level and hepatic metabolism of 4β-HC were not changed by KTZ. The inhibition of hepatic uptake of GCDCA-S by RIF was fully reversed after a 7-d washout of RIF. Plasma concentration and hepatic uptake ratio of GCDCA-S were correlated with the plasma level and hepatic uptake of ATV in rats with ANIT-induced liver injury, respectively. These results demonstrate that plasma GCDCA-S is a sensitive probe for the assessment of Oatps-mediated hepatic uptake of ATV. However, Cyp3a-mediated metabolism of ATV was not predicted by plasma 4β-HC levels in rats., Graphical abstract Image, graphical abstract

In this paper, in order to realize a representation of continuous domains, the notions of relationally consistent F-augmented contexts and relationally approximable concepts are introduced, which provides a generalized framework of formal concept analysis. We also introduce the notion of F-approximable mappings which serves as the morphism between relationally consistent F-augmented contexts. The main result is that the category of relationally consistent F-augmented contexts is equivalent to that of continuous domains with Scott continuous maps being morphisms. This provides a new approach to concretely representing continuous domains and demonstrates the efficiency of formal concept analysis in representing some important partially ordered structures.

Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.

Programmed cell death-ligand 1 (PD-L1) expression on tumor tissue has been associated with favorable response to anti-programmed cell death-receptor 1/PD-L1 therapy in many human cancers. Studies have reported that PD-L1 is also expressed in thyroid cancer. The objective of this paper is to introduce the potential predictive and therapeutic values of PD-L1 in thyroid cancer.A literature search was conducted in the PubMed database using the terms "PD-L1," "B7-H1," and "thyroid cancer." PD-L1 positivity was determined by immunohistochemical assay.The frequency of PD-L1 positivity in different studies ranged from 6.1 to 82.5% in papillary thyroid cancer (PTC) patients and 22.2 to 81.2% in anaplastic thyroid cancer (ATC) patients. PD-L1 positivity rate was higher in ATC than in PTC within the same studies, and its expression intensity was significantly higher in tumor tissue than in the corresponding nontumor thyroid tissues. Moreover, PD-L1 expression was positively associated with the aggressiveness and recurrence of thyroid cancers and negatively associated with the differentiation status and outcomes. PD-L1 checkpoint pathway blockade may emerge as a promising therapeutic target in the treatment of thyroid cancers.PD-L1 is a potential biomarker to predict the recurrence and prognosis of thyroid cancers. It is also a novel immunotherapy target for optimizing the management landscape of radioiodine-refractory and ATCs.ATC = anaplastic thyroid cancer; DTC = differentiated thyroid cancer; IHC = immunohistochemical; OS = overall survival; PD-1 = programmed cell death-receptor 1; PD-L1 = programmed cell death-ligand 1; PD-L2 = programmed cell death-ligand 2; PTC = papillary thyroid cancer; TNM = tumor-node-metastasis; Treg = regulatory T cell.

Objectives Gardenia Jasminoides Ellis (Zhizi), belonging to Rubiaceae family, has been traditionally used for treatment cholestasis and jaundice for centuries in Asian countries. In the theory of Traditional Chinese Medicines, Zhizi could dispel dampness and heat via the urine to execute its choleretic effects. However, the potential molecular mechanism has been still poorly clarified. Here, we investigated the effect of different dose of Zhizi aqueous extract powder (0.3 g/kg/d and 0.9 g/kg/d) on urinary excretion of bile acids (BAs), and defined the potential mechanism via renal BAs efflux transporters Mrp2 and Mrp4 in normal rats. Methods Male Wistar rats were orally administrated with 0.3 or 0.9 g/kg/d dose of Zhizi aqueous extract powder for 2 weeks, then body weight, serum aminotransferase, total BAs concentrations in liver, bile, serum, kidney and urine, 1 h bile flow, 12-h urinary volume, biliary and urinary excretion amount of total BAs as well as protein expression of major renal BAs efflux transporter Mrp2 and Mrp4, were all evaluated. Results Zhizi especially the high dose of Zhizi aqueous extract powder could reduce hepatic total BAs concentration. Additionally, bile flow and biliary excretion had no significant difference, but the remarkable increasing urinary excretion of BAs and 2 to 3 folds up-regulated renal Mrp2 expression were observed after administrated with Zhizi as compared with the control group. Conclusion The findings indicate that Zhizi reduces hepatic total BAs level by increasing urinary excretion rather than the biliary excretion of BAs, which, in turn ascribed to elevated protein expression of Mrp2 at apical membrane of renal tubular epithelial cells.

One of the basic challenges in developing structural methods for systematic audition on the quality of biomedical ontologies is the computational cost usually involved in exhaustive sub-graph analysis. We introduce ANT-LCA, a new algorithm for computing all non-trivial lowest common ancestors (LCA) of each pair of concepts in the hierarchical order induced by an ontology. The computation of LCA is a fundamental step for non-lattice approach for ontology quality assurance. Distinct from existing approaches, ANT-LCA only computes LCAs for non-trivial pairs, those having at least one common ancestor. To skip all trivial pairs that may be of no practical interest, ANT-LCA employs a simple but innovative algorithmic strategy combining topological order and dynamic programming to keep track of non-trivial pairs. We provide correctness proofs and demonstrate a substantial reduction in computational time for two largest biomedical ontologies: SNOMED CT and Gene Ontology (GO). ANT-LCA achieved an average computation time of 30 and 3 sec per version for SNOMED CT and GO, respectively, about 2 orders of magnitude faster than the best known approaches. Our algorithm overcomes a fundamental computational barrier in sub-graph based structural analysis of large ontological systems. It enables the implementation of a new breed of structural auditing methods that not only identifies potential problematic areas, but also automatically suggests changes to fix the issues. Such structural auditing methods can lead to more effective tools supporting ontology quality assurance work.

Accurate and rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is significant for early tracing, isolation, and treatment of infected individuals, which will efficiently prevent large-scale transmission of coronavirus disease 2019 (COVID-19). Here, two kinds of test strips for receptor binding domain (RBD) and N antigens of SARS-CoV-2 are established with high sensitivity and specificity, in which AIE luminogens (AIEgens) are utilized as reporters. Because of the high brightness and resistance to quenching in aqueous solution, the limit of detection can be as low as 6.9 ng/mL for RBD protein and 7.2 ng/mL for N protein. As an antigen collector, an N95 mask equipped with a test strip with an excellent enrichment effect would efficiently simplify the sampling procedures. Compared with a test strip based on Au nanoparticles or fluorescein isothiocyanate (FITC), the AIEgen-based test strip shows high anti-interference capacity in complex biosamples. Therefore, an AIEgen-based test strip assay could be built as a promising platform for emergency use during the pandemic., Graphical Abstract, Zhang et al. report a general test strip platform based on AIE luminogens as a reporter for SARS-CoV-2 antigen detection. The assay is a rapid, scale-up detection tool for SARS-CoV-2 screening with high sensitivity and specificity and good reproducibility without the need for expensive machines or highly trained personnel.

The selective valorization of lignite into monocyclic aromatic compounds (MCACs) is extremely challenging due to its chemical inertness and geometrical complexity. The catalytic efficiency of lignite valorization into MCACs over solid acids is significantly reduced by the presence of H2O resulting in the leaching and deactivation of acid sites. Moreover, the precise fabrication of poly(ionic liquid)s (PILs) containing Bronsted-Lewis acidic sites, well-defined mesoporous channels, and hydrophobicity remains a considerable challenge. Herein, a novel hydrophobic mesoporous PILs with strong Bronsted-Lewis acid sites was successfully constructed by a synergistic regulation-induced copolymerization strategy for the first time. More exotically, the resultant multifunctional PILs was found to be ultra-efficient catalyst for the selective valorization of Yiwu lignite (YL) into MCACs with 23.5 wt% yield, which is the highest yield reported for lignite catalytic valorization by precious metal-free catalysts under mild conditions. The co-catalysis mechanisms of YL valorization into MCACs over the multifunctional PILs are confirmed by characterization methods and the synergistic catalysis mechanisms are as follows: (1) hydrophobic micro-environment: the hydrophobic micro-environment created by hydrophobic block is favorable for preventing the leaching and deactivation of Bronsted-Lewis acid sites; (2) mesoporous confinement: the well-defined mesoporous channels strengthen the adsorption amount of H2 and increases the concentration of substrates; (3) synergistic catalytic active hydrogen transfer of Bronsted-Lewis acid sites: Bronsted-Lewis acid sites synergistically promote H2 heterolysis to the mobile H+ and immobile H−, and then the resulting mobile H+ transfers to oxygen atom in lignite to produce MCACs via C–O bond cleavage. This work not only sheds some light on developing the multifunctional solid acid catalysts, but also demonstrates an efficient catalyzing method to produce lignite-based MCACs by co-catalysis of Bronsted-Lewis acidic sites, mesoporous confinement, and hydrophobic micro-environment.

Objective We introduce a structural-lexical approach for auditing SNOMED CT using a combination of non-lattice subgraphs of the underlying hierarchical relations and enriched lexical attributes of fully specified concept names. Our goal is to develop a scalable and effective approach that automatically identifies missing hierarchical IS-A relations. Methods Our approach involves 3 stages. In stage 1, all non-lattice subgraphs of SNOMED CT’s IS-A hierarchical relations are extracted. In stage 2, lexical attributes of fully-specified concept names in such non-lattice subgraphs are extracted. For each concept in a non-lattice subgraph, we enrich its set of attributes with attributes from its ancestor concepts within the non-lattice subgraph. In stage 3, subset inclusion relations between the lexical attribute sets of each pair of concepts in each non-lattice subgraph are compared to existing IS-A relations in SNOMED CT. For concept pairs within each non-lattice subgraph, if a subset relation is identified but an IS-A relation is not present in SNOMED CT IS-A transitive closure, then a missing IS-A relation is reported. The September 2017 release of SNOMED CT (US edition) was used in this investigation. Results A total of 14,380 non-lattice subgraphs were extracted, from which we suggested a total of 41,357 missing IS-A relations. For evaluation purposes, 200 non-lattice subgraphs were randomly selected from 996 smaller subgraphs (of size 4, 5, or 6) within the “Clinical Finding” and “Procedure” sub-hierarchies. Two domain experts confirmed 185 (among 223) suggested missing IS-A relations, a precision of 82.96%. Conclusions Our results demonstrate that analyzing the lexical features of concepts in non-lattice subgraphs is an effective approach for auditing SNOMED CT.

An efficient protocol for preparation of rare L-idose derivatives from 5-OH D-glucofuranose derivatives was developed, and the stereo-inversion of 5-OH was assisted by neighboring acyl group. A library of L-idose derivatives with various protective groups at C3 and C6 positions were obtained from the corresponding D-glucofuranose derivatives in good to high yields, which provides an alternative approach for the synthesis of L-iduronic acid building blocks when assembling heparin-like oligosaccharides. And the mechanism of the stereo-inversion reaction was proposed.

Fondaparinux, a synthetic pentasaccharide anticoagulant based on heparin antithrombin-binding domain, is derived from a chemical synthesis with more than 50 steps. Herein, we identified nine analogues separated from commercially available crude fondaparinux sodium, and tested their anticoagulant activity in vitro. Based on the activity results, the most active derivative Rrt1.17 was chemically synthesized. Biological properties in vitro and in vivo indicated that the well-defined derivative Rrt1.17 was a more efficient anticoagulant candidate compared with fondaparinux.

The CuCe/AC catalysts were prepared by impregnation first with Ce and then with Cu, and effect of calcination temperature on catalytic performance of the CuCe/AC catalysts for gas-phase oxidative carbonylation of methanol to dimethyl carbonate was studied. The active component content and valence state of as-prepared catalysts were characterized by XRD, XPS and H2-TPR. The results show that Cu2+ is gradually reduced to Cu+ and Cu0 species. After calcinated at 450°C, some Cu2O phase still exists in the catalyst, which indicates that interaction between Cu and Ce has suppressed the reduction of Cu2O. As the calcination temperature of 300°C, the content of Cu+ achieves the highest, and the corresponding catalyst shows the best catalytic activity. The space-time yield of DMC, selectivity of DMC and conversion of methanol are 143.4 mg/(g·h), 85.2% and 4.1%, respectively.

Postsurgical management of differentiated thyroid cancer in China has gained a great success in the last twenty years, but there are still gaps to be filled. Here, we briefly review the current status and also extend an outlook for future development.

Identifying epileptic seizures through analysis of the electroencephalography (EEG) signal becomes a standard method for the diagnosis of epilepsy. Manual seizure identification on EEG by trained neurologists is time-consuming, labor-intensive and a reliable automatic seizure/non-seizure classification method is needed. One of the challenges in automatic seizure/non-seizure classification is that seizure morphologies exhibit considerable variabilities. In order to capture essential seizure patterns, this paper leverages an attention mechanism and a bidirectional long short-term memory (BiLSTM) to exploit both spatial and temporal discriminating features and overcome seizure variabilities. The attention mechanism captures spatial features according to the contributions of different brain regions to seizures. BiLSTM extracts discriminating temporal features in forward and backward directions. Cross-validation experiments and cross-patient experiments over the noisy data of CHB-MIT were performed. We obtained average sensitivity of 87.30%, specificity of 88.30% and precision of 88.29% in cross-validation experiments, higher than using the current state-of-the-art methods, and the standard deviations were lower. These results indicate that our approach performs well against current state-of-the-art methods and is more robust across patients.

Complicated multifactorial diseases deteriorate from one disease to other diseases. For example, existing studies consider Alzheimer’s disease (AD) a co-morbidity of epilepsy, but also recognize epilepsy to occur more frequently in patients with AD than those without. It is important to understand the progress of disease that deteriorates to severe diseases. To this end, we develop a transitional phenotyping method based on both longitudinal and cross-sectional relationships between diseases and/or medications. For a cross-sectional approach, we utilized a skip-gram model to represent co-occurred disease or medication. For a longitudinal approach, we represented each patient as a transition probability between medical events and used supervised tensor factorization to decompose into groups of medical events that develop together. Then we harmonized both information to derive high-risk transitional patterns. We applied our method to disease progress from epilepsy to AD. An epilepsy-AD cohort of 600,000 patients were extracted from Cerner Health Facts data. Our experimental results suggested a causal relationship between epilepsy and later onset of AD, and also identified five epilepsy subgroups with distinct phenotypic patterns leading to AD. While such findings are preliminary, the proposed method combining representation learning with tensor factorization seems to be an effective approach for risk factor analysis.

The Cleisostoma–Gastrochilus clades are among the most speciose and diverse groups of Asian orchids and are a taxonomically problematic group. Phylogenetic relationships among the genera of these clades have remained unresolved with traditional sequences from one or a few markers. We present large-scale phylogenomic data sets, incorporating complete chloroplast genome sequences from 53 species (including 41 species sequenced in this study), to compare plastome structure and to resolve the phylogenetic relationships of these clades. The plastomes of Cleisostoma–Gastrochilus clades possessed the quadripartite structure and plastome genes of typical angiosperms with sizes ranging from 142 to 149 kb and encoding a set of 118–120 genes. Unusual structural features were detected in the plastome of Uncifera acuminata, including the presence of a large 17-kb inversion (19 genes) in the Large Single-Copy region and the loss of the rpl32 gene in Cleisostoma fuerstenbergianum. The pseudogenization of ndh genes was widespread in these clades. Phylogenomic analyses, including 68 plastid protein-coding genes, showed that these clades can be subdivided into three major groupings and six subgroupings: Vandopsis undulata, the Gastrochilus clade (including the Trichoglottis and Gastrochilus subclades) and the Cleisostoma clade (including the Vandopsis, Diploprora, Cleisostoma and Schoenorchis subclades). Two genera, Vandopsis and Cleisostoma, were not monophyletic. A new genus, Cymbilabia, was proposed to avoid non-monophyly of Vandopsis. Our results demonstrate the power of plastid phylogenomics to improve the phylogenetic relationships of intricate groups and provide new insight into plastome evolution in Orchidaceae.

The phosphoenolpyruvate carboxylase (PEPC) gene is the key enzyme in CAM and C4 photosynthesis. A detailed phylogenetic analysis of the PEPC family was performed using sequences from 60 available published plant genomes, the Phalaenopsis equestris genome and RNA-Seq of 15 additional orchid species. The PEPC family consists of three distinct subfamilies, PPC-1, PPC-2, and PPC-3, all of which share a recent common ancestor in chlorophyte algae. The eudicot PPC-1 lineage separated into two clades due to whole genome duplication (WGD). Similarly, the monocot PPC-1 lineage also divided into PPC-1M1 and PPC-1M2 through an ancient duplication event. The monocot CAM- or C4-related PEPC originated from the clade PPC-1M1. WGD may not be the major driver for the performance of CAM function by PEPC, although it increased the number of copies of the PEPC gene. CAM may have evolved early in monocots, as the CAM-related PEPC of orchids originated from the monocot ancient duplication, and the earliest CAM-related PEPC may have evolved immediately after the diversification of monocots, with CAM developing prior to C4. Our results represent the most complete evolutionary history of PEPC genes in green plants to date and particularly elucidate the origin of PEPC in orchids.

Neutron-induced reactions on Al-27 and F-19 nuclei are investigated using the optical model implemented in the TALYS 1.4 toolkit. Incident neutron energies in a wide range from 0.1 key to 30 MeV are calculated. The cross sections for the main channels (n, np), (n, p), (n, alpha), (n, 2n), and (n, gamma) and the total reaction cross section (n, tot) of the reactions are obtained. When the default parameters in TALYS 1.4 are adopted, the calculated results agree with the measured results. Based on the calculated results for the n + Al-27 and n + F-19 reactions, the results of the n + Al-27 F-19 reactions are predicted. These results are useful both for the design of thorium-based molten salt reactors and for neutron activation analysis techniques. (C) 2015 Elsevier B.V. All rights reserved.

The subtribe Aeridinae, which contains approximately 90 genera, is one of the most diverse and taxonomically puzzling groups in Orchidaceae. In the present study, the phylogenetic relationships of Aeridinae were reconstructed utilizing five DNA sequences (ITS, atpI-H, matK, psbA-trnH, and trnL-F) from 211 taxa in 74 genera. The results of the phylogenetic analyses indicate that Aeridinae is monophyletic and that the subtribe can primarily be grouped into 10 clades: (1) Saccolabium clade, (2) Chiloschista clade, (3) Phalaenopsis clade, (4) Thrixspermum clade, (5) Vanda clade, (6) Aerides clade, (7) Trichoglottis clade, (8) Abdominea clade, (9) Gastrochilus clade, and (10) Cleisostoma clade. In our examination, most genera of Aeridinae were well-supported as monophyletic, and several genera, namely, Pteroceras, Cleisostoma, Vandopsis, Diploprora, Malleola, and Robiquetia, were found to be polyphyletic as currently circumscribed. In addition, several classifications of intra-genera, such as the subgenus Codonosepalum of Taeniophyllum and the section Gastrochilus of Gastrochilus, were also revealed to be paraphyletic. Due to the many questions raised by our phylogenies, the present study may serve as a reference for future taxonomic studies of Aeridinae.

Display Omitted Systematic studies of disease phenotype networks can discover new disease genes.Current disease phenotype networks are largely incomplete.We created a new Disease Manifestation Network (DMN) from biomedical ontologies.We compared DMN with genetic networks and a widely-used phenotype network.DMN reflects genetic associations among diseases and contains novel knowledge. Systems approaches to analyzing disease phenotype networks in combination with protein functional interaction networks have great potential in illuminating disease pathophysiological mechanisms. While many genetic networks are readily available, disease phenotype networks remain largely incomplete. In this study, we built a large-scale Disease Manifestation Network (DMN) from 50,543 highly accurate disease-manifestation semantic relationships in the United Medical Language System (UMLS). Our new phenotype network contains 2305 nodes and 373,527 weighted edges to represent the disease phenotypic similarities. We first compared DMN with the networks representing genetic relationships among diseases, and demonstrated that the phenotype clustering in DMN reflects common disease genetics. Then we compared DMN with a widely-used disease phenotype network in previous gene discovery studies, called mimMiner, which was extracted from the textual descriptions in Online Mendelian Inheritance in Man (OMIM). We demonstrated that DMN contains different knowledge from the existing phenotype data source. Finally, a case study on Marfan syndrome further proved that DMN contains useful information and can provide leads to discover unknown disease causes. Integrating DMN in systems approaches with mimMiner and other data offers the opportunities to predict novel disease genetics. We made DMN publicly available at nlp/case.edu/public/data/DMN.

Functional exercise after total knee arthroplasty (TKA) is necessary. However, it may be a difficult and painful process for the patient. Desirable methods of relieving the patient's pain are worth exploring. Oral supplement of adenosine triphosphate (ATP) is a potential option. In the present study, we decide to investigate whether short-term administration of ATP benefits patients undergoing TKA. A total of 244 subjects were randomized to receive 120mg ATP or placebo each day for 4weeks. Significant differences in quadriceps strength, pain scores at postoperative days 7, 14, 21, and 28 and total opioid consumption were detected. It follows that oral supplement of ATP could benefit patients recovering from TKA.

Display Omitted An effective pipeline for extracting complex epilepsy phenotypes is developed.MetaMap is successfully adapted to detect anatomic locations related to epilepsy.Epilepsy named entity is extracted with the use of regular expressions.Regular expressions are automatically generated based on a domain ontology.An ontology-driven interface is used for querying complex epilepsy phenotypes. Epilepsy is a common serious neurological disorder with a complex set of possible phenotypes ranging from pathologic abnormalities to variations in electroencephalogram. This paper presents a system called Phenotype Exaction in Epilepsy (PEEP) for extracting complex epilepsy phenotypes and their correlated anatomical locations from clinical discharge summaries, a primary data source for this purpose. PEEP generates candidate phenotype and anatomical location pairs by embedding a named entity recognition method, based on the Epilepsy and Seizure Ontology, into the National Library of Medicine's MetaMap program. Such candidate pairs are further processed using a correlation algorithm. The derived phenotypes and correlated locations have been used for cohort identification with an integrated ontology-driven visual query interface. To evaluate the performance of PEEP, 400 de-identified discharge summaries were used for development and an additional 262 were used as test data. PEEP achieved a micro-averaged precision of 0.924, recall of 0.931, and F 1 -measure of 0.927 for extracting epilepsy phenotypes. The performance on the extraction of correlated phenotypes and anatomical locations shows a micro-averaged F 1 -measure of 0.856 (Precision: 0.852, Recall: 0.859). The evaluation demonstrates that PEEP is an effective approach to extracting complex epilepsy phenotypes for cohort identification.

Objectives To learn the prevalence of the primary classical broad-host-range (BHR) IncA/C, IncN, IncP, IncQ, and IncW plasmids in dominant gram-negative bacilli from inpatients in a teaching hospital in southern China. Methods A multiplex polymerase chain reaction based on the replicons of BHR IncA/C, IncN, IncP, IncQ, and IncW plasmids was developed and used to determine these BHR plasmids. The difference in prevalence rates among the different species from three specimens was evaluated by a binary logistic regression model and the differences between multidrug-resistant organisms (MDRO) and non-MDRO were assessed using a chi-square test. Results The average positive detection percentages of the replicons were 4.3%, 3.7%, 3.0%, 2.6%, and 1.9%, respectively, for IncN, IncP, IncQ, IncW, and IncA/C in descending order. The distribution of all five BHR plasmids did not differ significantly between specimens collected from wounds and urine, although both were significantly higher than those of sputum. The prevalence rates of all five BHR plasmids in MDROs were significantly higher than those in non-MDRO for Enterobacteriaceae; however, no significant difference was seen in non-fermenting gram-negative bacilli (NFGNB). Conclusions BHR IncA/C, IncN, IncP, IncQ, and IncW plasmids, which occur more often in bacilli from wound and urine specimens than those of sputum, are widespread in Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Enterobacter cloacae, Pseudomonas aeruginosa, and Acinetobacter baumannii strains isolated from inpatients. The prevalence rates in MDRO are higher than those in non-MDRO for Enterobacteriaceae but not significantly different for NFGNB.

A new liquid chromatography–tandem mass spectrometry (LC–MS/MS) method by using dynamic multiple reaction monitoring (DMRM) has been developed and validated for the simultaneous determination of digoxin (DGX) and six main components of Ginkgo biloba leaf extract (GBE) in rat plasma. Comparing with the conventional multiple reaction monitoring (MRM), DMRM dramatically decreases the number of concurrent MRM transitions, and significantly extended the dwell time, which provided much higher sensitivity and reproducibility than MRM when complex multi-component samples were quantified. The plasma samples were protein precipitated with methanol, the detection was accomplished with electro-spray ionization (ESI) as the ion source operating in the negative ionization mode, with methanol and water as mobile phase, and with an Agilent Zorbax eclipse plus C18 column (4.6 × 100 mm, 3.5 μm) as the analytical column. The total run time was 12.0 min. The validation of the method was implemented including specificity, linearity, accuracy, precision, recovery, matrix effect and stability. This method was successfully applied to the herb–drug pharmacokinetic interaction study of DGX combined with GBE after oral administration to rats. The result indicated that co-administration of GBE and DGX significantly influenced the pharmacokinetics of DGX when compared to that of single DGX-treated rats.

Goodyerinae are one of the most species-rich and widespread subtribes of Orchidaceae but notorious for their taxonomic difficulty. Here, a comprehensive molecular phylogenetic study of the subtribe is presented based on two nuclear (ITS, Xdh) and five plastid (matK, psaB, rbcL, trnL, trnL-F) regions. A total of 119 species were included representing all clades recovered by previous phylogenetic analyses as well as seven outgroups. Maximum parsimony, maximum likelihood and Bayesian inference methods were used to infer the phylogenetic relationships. The results show that the Goodyerinae subdivided into three major subdivisions and six groupings: Pachyplectron, Goodyera clade (including Goodyera procera, Microchilus subclade and Goodyera subclade) and Cheirostylis clade (including Gonatostylis, Cheirostylis subclade and Ludisia subclade). Four genera, Erythrodes, Goodyera, Myrmechis and Odontochilus, are not monophyletic. The results support Odontochilus s. l. to include Myrmechis and Kuhlhasseltia. The systematic positions of Goodyera procera and two isolated genera, Herpysma and Orchipedum, are difficult to determine.

With a large percentage of clinical trials still using paper forms as the primary data collection tool, there is much potential for increasing efficiency through web-based data collection systems, especially for large-scale multi-center trials. This paper presents OnWARD, an ontology-driven, secure, rapidly-deployed, web-based framework supporting data capture for large-scale multi-center clinical research. Our approach is developed using the agile methodology to provide a flexible, user-centered dynamic form generator, which can be quickly deployed and customized for any clinical study without the need of deep technical expertise. Because of the flexible framework, the data management system can be extended to accommodate a large variety of data types, including genetic, genomic and proteomic data. In this paper, we demonstrate the initial deployment of OnWARD for a Phase II multi-center clinical trial after a development period of merely three months. The study utilizes 23 clinical report forms containing more than 1500 data points. Preliminary evaluation results show that OnWARD exceeded expectations of the clinical investigators in efficiency, flexibility and ease in setting up.

We introduce a framework for the study of formal contexts and their lattices induced by the additional structure of self-relations on top of the traditional incidence relation. The induced contexts use subsets as objects and attributes, hence the name power context and power concept. Six types of new incidence relations are introduced by taking into account all possible combinations of universal and existential quantifiers as well as the order of the quantifications in constructing the lifted power contexts. The structure of the power concept lattice is investigated through projection mappings from the baseline objects and attributes to those of the power context, respectively. We introduce the notions of extensional consistency and intensional consistency, corresponding to the topological notions of continuity in the analogous setting when concepts are viewed as closed sets. We establish Galois connections for these notions of consistency. We further introduce the notion of faithfulness for the first type of lifted incidence relation based on the fact that it can be equivalently characterized by a concept-faithful morphism. We also present conditions under which the power concept lattice serves as a factor lattice of the base concept lattice.

A new inorganic–organic hybrid compound [FTMA]2[Co(NCS)4] (FTMA = ferrocenylmethyltrimethylammonium cation) has been synthesized and characterized by IR, UV, elemental analysis and X-ray crystallography. Co(II) atom has a distorted tetrahedral environment with four N atoms of four NCS− anions. In the solid state there are C–H⋯π interactions between adjacent ferrocenyl cations, which generate one-dimensional (1-D) supramolecular chain, and C–H⋯S hydrogen bonds between [FTMA]+ cations and cobalt thiocyanate anions. The title compound shows strong purple fluorescence emission in the solid state at room temperature.

Two procedures for computing closures in binary partial algebras (BPA) are introduced: a Fibonacci-style procedure for closures in associative BPAs, and a multistage procedure for closures in associative, commutative and idempotent BPAs. Ramifications in areas such as resolution theorem proving, graph-theoretic algorithms, formal languages and formal concept analysis are discussed. In particular, the multistage procedure, when applied to formal concept analysis, results in a new algorithm outperforming leading algorithms for computing concept sets.

We developed a device for the treatment of Ficat and Arlet stage II and III osteonecrosis of the femoral head. This device, which we named the "super-elastic cage," was designed to provide mechanical support for the necrotic weight-bearing area of the femoral head to prevent its collapse. The cage was used in combination with surgical removal of necrotic bone, insertion of vascularized pedical bone graft, or impacted autologous cancellous bone graft. A total of 93 hips in 62 patients at Ficat stage II to III were included in a 8-year study. Implantations were performed by 2 different approaches: Smith-Peterson approach and minimal invasive approach by the lateral side of great trochanter. The follow-up period was between 72 and 107 months. Of the femoral heads in this study, 82.7% survived. The superelastic cage implantation technique may offer an alternative treatment to the early and middle stages of osteonecrosis of the femoral head.

The electron emission characteristics of PLZT 8/65/35 ferroelectric are studied. High current density has been obtained from PLZT 8/65/35 ferroelectric cathode. The source of the disturbance in the experiment is discussed and several methods to reduce the disturbance are proposed. It is discovered that there is a voltage threshold, and the electron emission will not occur until the amplitude of the pulse exceeds the threshold. Moreover, there are two current peaks in the FE electron emission curves, the primary peak remains stable in location and intensity, while the secondary one shows instability during repeating experiments.

This paper studies maximality and totality of stable functions in the category of stable bifinite domains. We present three main results as follows,o(1)every maximum-preserving function is a maximal element in the stable function spaces;(2)a maximal stable function f : D → E is maximum-preserving if D is maximum-separable and E is completely separable; and(3)a stable bifinite domain D is maximum-separable if and only if for any locally distributive stable bifinite domain E, each maximal stable function f : D → E is maximum-preserving.

More than a dozen years ago, Amadio [Bifinite domains: stable case, in: Lecture Notes in Computer Science, vol. 530, 1991, pp. 16-33] (see Amadio and Curien, Domains and Lambda-Calculi, Cambridge Tracts in Theoretical Computer Science, vol. 46, Cambridge University Press, 1998 as well) raised the question of whether the category of stable bifinite domains of Amadio-Droste [R.M. Amadio, Bifinite domains: stable case, in: Lecture Notes in Computer Science, vol. 530, 1991, pp. 16-33; M. Droste, On stable domains, Theor. Comput. Sci. 111 (1993) 89-101; M. Droste, Cartesian closed categories of stable domains for polymorphism, Preprint, Universitat GHS Essen] is the largest cartesian closed full sub-category of the category of @w-algebraic meet-cpos with stable functions. An affirmative solution to this problem has two major steps: (1) Show that for any @w-algebraic meet-cpo D, if all higher-order stable function spaces built from D are @w-algebraic, then D is finitary (i.e., it satisfies the so-called axiom I); (2) Show that for any @w-algebraic meet-cpo D, if D violates MI^~, then [D->D] violates either M or I. We solve the first part of the problem in this paper, i.e., for any @w-algebraic meet-cpo D, if the stable function space [D->D] satisfies M, then D is finitary. Our notion of (mub, meet)-closed set, which is introduced for step 1, will also be used for treating some example cases in step 2.

This paper introduces power default reasoning (PDR), a framework for non-monotonic reasoning based on the domain-theoretic idea of modeling default rules with partial-information in a higher-order setting. PDR lifts a non-monotonic operator at the base (syntactic) level to a well-behaved, almost monotonic operator in the higher-order space of the Smyth power-domain—effectively a space of sets of models. Working in the model space allows us to prove the dichotomy theorem and the extension splitting theorem, leading to a more well-behaved logic and (modulo the usual complexity conjectures) a less complex logic than standard default logic. Specifically, we prove that skeptical normal default inference is a problem complete for co-NP(3) in the Boolean hierarchy for strict propositional logic and NP(4)-complete in general. These results (by changing the underlying semantics) contrasts favorably with similar results of Gottlob (J. Logic Comput. 2(3) (1992) 397–425), who proves that standard skeptical default reasoning is Π2P-complete. Furthermore, we show that the skeptical non-monotonic consequence relation, defined using our domain-theoretic semantics, obeys all of the laws for preferential consequence relations defined by Kraus, Lehmann, and Magidor. In particular, we get the property of being able to reason by cases, and the so-called law of cautious monotony. Both of these laws fail for the standard propositional default logic of Reiter (Artificial Intelligence 13 (1980) 81–132), but hold in PDR as a consequence of the dichotomy theorem and the extension splitting theorem.

This note presents a concrete representation of stably compact spaces. This is used to give a simple, and predicative, description of the patch topology of a stably compact space (J. Pure Appl. Algebra, to appear).

This paper serves to bring three independent but important areas of computer science to a common meeting point: Formal Concept Analysis (FCA), Chu Spaces, and Domain Theory (DT). Each area is given a perspective or reformulation that is conducive to the flow of ideas and to the exploration of cross-disciplinary connections. Among other results, we show that the notion of states in Scott’s information system corresponds precisely to that of formal concepts in FCA with respect to all finite Chu spaces, and the entailment relation corresponds to “association rules”.

This note proves a useful characterization of spectral frames: a frame is spectral if and only if it can be generated from a compact coverage relation, where compactness is defined in the usual topological sense.

We introduce a domain-theoretic foundation for disjunctive logic programming. This foundation is built on clausal logic, a representation of the Smyth powerdomain of any coherent algebraic dcpo. We establish the completeness of a resolution rule for inference in such a clausal logic; we introduce a natural declarative semantics and a fixed-point semantics for disjunctive logic programs, and prove their equivalence; finally, we apply our results to give both a syntax and semantics for default logic in any coherent algebraic dcpo. 2001 Elsevier Science

This paper presents a Boolean-matrix-based method to automata theory, with an application to the study of regularity-preserving functions. A new characterization of such functions is derived in terms of the property of ultimate periodicity with respect to powers of Boolean matrices. This characterization reveals the intrinsic algebraic nature of regularity-preserving functions. It facilitates a concise proof of known, as well as previously unknown, properties of regularity-preserving functions, leading to the solution of the “subtraction problem,” left open by Kosaraju.